+Open data
-Basic information
Entry | Database: PDB / ID: 2ijk | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of a Rom protein dimer at 1.55 angstrom resolution | ||||||
Components | Regulatory protein rop | ||||||
Keywords | TRANSCRIPTION REGULATOR / Rom / Rop / ColE1 plasmid copy control | ||||||
Function / homology | Helix Hairpins - #230 / Regulatory protein Rop / Rop-like superfamily / Rop protein / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / identical protein binding / Regulatory protein rop Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Struble, E.B. | ||||||
Citation | Journal: Proteins / Year: 2008 Title: New crystal structures of ColE1 Rom and variants resulting from mutation of a surface exposed residue: Implications for RNA-recognition. Authors: Struble, E.B. / Ladner, J.E. / Brabazon, D.M. / Marino, J.P. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2ijk.cif.gz | 62.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2ijk.ent.gz | 47.1 KB | Display | PDB format |
PDBx/mmJSON format | 2ijk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ijk_validation.pdf.gz | 441.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2ijk_full_validation.pdf.gz | 443 KB | Display | |
Data in XML | 2ijk_validation.xml.gz | 8.8 KB | Display | |
Data in CIF | 2ijk_validation.cif.gz | 12.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ij/2ijk ftp://data.pdbj.org/pub/pdb/validation_reports/ij/2ijk | HTTPS FTP |
-Related structure data
Related structure data | 2ijhC 2ijiC 2ijjC 1ropS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 7162.896 Da / Num. of mol.: 2 / Mutation: M1G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rop / Plasmid: pET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21(DE3) / References: UniProt: P03051 #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.82 Å3/Da / Density % sol: 32.49 % |
---|---|
Crystal grow | Method: vapor diffusion, hanging drop / pH: 6 Details: Hanging drop contained 1 uL protein/RNA mixture (0.3 0.4 mM complex) and 1 uL well buffer (50 mM sodium cacodylate pH 6.0, 0.1 M potassium chloride, 25 mM magnesium chloride, and 15% ...Details: Hanging drop contained 1 uL protein/RNA mixture (0.3 0.4 mM complex) and 1 uL well buffer (50 mM sodium cacodylate pH 6.0, 0.1 M potassium chloride, 25 mM magnesium chloride, and 15% isopropanol)., VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 105 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 2, 2006 / Details: Blue Max-flux confocal mirrors |
Radiation | Monochromator: confocal mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→100 Å / Num. obs: 14338 / % possible obs: 94.8 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Rmerge(I) obs: 0.072 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 1.55→1.61 Å / Rmerge(I) obs: 0.244 / Mean I/σ(I) obs: 2.7 / Num. unique all: 913 / % possible all: 60.6 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1ROP Resolution: 1.55→48.91 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.929 / SU B: 3.494 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.462 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→48.91 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.55→1.59 Å / Total num. of bins used: 20
|